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;NB newest version is on ANGSD github
Small ultrafast program for estimating the read length and get the insert size from uncompressed samples:
Small ultrafast program for estimating the read length and get the insert size from uncompressed samples:


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It's a faithful implementation of this script [http://allaboutbioinfo.blogspot.dk/2012/04/estimating-paired-end-read-insert.html]
It's a faithful implementation of this script [http://allaboutbioinfo.blogspot.dk/2012/04/estimating-paired-end-read-insert.html]
It only uses the paired end reads that have a perfect match, and where the pair matches the same chromosome.
=Installation=
=Installation=
<pre>
<pre>

Latest revision as of 08:02, 18 September 2014

NB newest version is on ANGSD github


Small ultrafast program for estimating the read length and get the insert size from uncompressed samples:

[1]

It's a faithful implementation of this script [2]

It only uses the paired end reads that have a perfect match, and where the pair matches the same chromosome.

Installation

wget http://www.popgen.dk/software/download/getinsertsize.cpp
g++ getinsertsize.cpp -O3 -o getinsertsize


Example

samtools view /home/thorfinn/data/victor/Merge/011557_RG.bam|head -n500000|./getinsertsize
Read length mean:95.677839	 sqrt(var):6.814545
Read span mean:169.868832	 sqrt(var):75.951989